Long-term data storage in DNA.

This article discusses how DNA might be used to store data. It is argued that, at present, DNA would be best employed as a long-term repository (thousands or millions of years). How data-containing DNA might be packaged and how the data might be encrypted, with particular attention to the encryption of written information, is also discussed. Various encryption issues are touched on, such as how data-containing DNA might be differentiated from genetic material, error detection, data compression and reading frame location. Finally, this article broaches the difficulty of constructing very large pieces of DNA in the laboratory and highlights some complications that might arise when attempting to transmit DNA-encrypted data to recipients who are a long period of time in the future.     

Uncertainties in synthetic DNA-based data storage

Deoxyribonucleic acid (DNA) has evolved to be a naturally selected, robust biomacromolecule for gene information storage, and biological evolution and various diseases can find their origin in uncertainties in DNA-related processes (e.g. replication and expression). Recently, synthetic DNA has emerged as a compelling molecular media for digital data storage, and it is superior to the conventional electronic memory devices in theoretical retention time, power consumption, storage density, and so forth. However, uncertainties in the in vitro DNA synthesis and sequencing, along with its conjugation chemistry and preservation conditions can lead to severe errors and data loss, which limit its practical application. To maintain data integrity, complicated error correction algorithms and substantial data redundancy are usually required, which can significantly limit the efficiency and scale-up of the technology. Herein, we summarize the general procedures of the state-of-the-art DNA-based digital data storage methods (e.g. write, read, and preservation), highlighting the uncertainties involved in each step as well as potential approaches to correct them. We also discuss challenges yet to overcome and research trends in the promising field of DNA-based data storage.     

Cytogenetic genotype-phenotype studies: improving genotyping, phenotyping and data storage

High-resolution molecular cytogenetic techniques such as genomic array CGH and MLPA detect submicroscopic chromosome aberrations in patients with unexplained mental retardation. These techniques rapidly change the practice of cytogenetic testing. Additionally, these techniques may improve genotype-phenotype studies of patients with microscopically visible chromosome aberrations, such as Wolf-Hirschhorn syndrome, 18q deletion syndrome and 1p36 deletion syndrome. In order to make the most of high-resolution karyotyping, a similar accuracy of phenotyping is needed to allow researchers and clinicians to make optimal use of the recent advances. International agreements on phenotype nomenclature and the use of computerized 3D face surface models are examples of such improvements in the practice of phenotyping patients with chromosomal anomalies. The combination of high-resolution cytogenetic techniques, a comprehensive, systematic system for phenotyping and optimal data storage will facilitate advances in genotype-phenotype studies and a further deconstruction of chromosomal syndromes. As a result, critical regions or single genes can be determined to be responsible for specific features and malformations.     

Genome mapping databases: data acquisition, storage and access.

The introduction of the genome database to the human gene mapping community in September 1990 heralded the advent of a new generation of databases to serve the needs of the human genome initiative over the coming years. The databases will act as a fulcrum around which the activities of the human genome initiative can be coordinated at an international level.     

Enabling secure auditing and deduplicating data without owner-relationship exposure in cloud storage

The public cloud storage auditing with deduplication has been studied to assure the data integrity and improve the storage efficiency for cloud storage in recent years. The cloud, however, has to store the link between the file and its data owners to support the valid data downloading in previous schemes. From this file-owner link, the cloud server can identify which users own the same file. It might expose the sensitive relationship among data owners of this multi-owners file, which seriously harms the data owners’ privacy. To address this problem, we propose an identity-protected secure auditing and deduplicating data scheme in this paper. In the proposed scheme, the cloud cannot learn any useful information on the relationship of data owners. Different from existing schemes, the cloud does not need to store the file-owner link for supporting valid data downloading. Instead, when the user downloads the file, he only needs to anonymously submit a credential to the cloud, and can download the file only if this credential is valid. Except this main contribution, our scheme has the following advantages over existing schemes. First, the proposed scheme achieves the constant storage, that is, the storage space is fully independent of the number of the data owners possessing the same file. Second, the proposed scheme achieves the constant computation. Only the first uploader needs to generate the authenticator for each file block, while subsequent owners do not need to generate it any longer. As a result, our scheme greatly reduces the storage overhead of the cloud and the computation overhead of data owners. The security analysis and experimental results show that our scheme is secure and efficient.     

Future-proof: bunkered data centres and the selling of ultra-secure cloud storage

Abandoned after the Cold War, nuclear bunkers around the world have found afterlives as ultra-secure data storage sites for cloud computing providers. The operators of these bunkered data centres capitalize on the spatial, temporal, and material security affordances of their subterranean fortresses, promoting them as ‘future-proof’ cloud storage solutions. Taking the concept of ‘future-proofing’ as its entry-point, this essay explores how data centre professionals work with the imaginative properties of the bunker to configure data as an object to be securitized. The essay takes the form of an ethnographic tour through a UK-based data bunker. During this tour, threatening data futures and fragile data materialities are conjured in order to secure the conditions of possibility for the bunkered data centre's commercial continuity. Future-proofing, it is argued, provides a conceptual opening onto the entangled imperatives of security and marketing that drive the commercial data storage industry.     

Use of a computer data file for storage of heat resistance data on bacterial spores

The use of a computer data file to compile published heat resistance data on bacterial spores is described. Information relating to sporulation, heating and recovery of the spores, in addition to decimal reduction times at different temperatures has been stored. The data file was constructed using Minitab and an indexer program on a VAX 11/750 computer operating on VMS. Storage of the data in this way enables rapid manipulation and analysis of large quantities of information relating to heat resistance of bacterial spores.     

Alignment-based approach for durable data storage into living organisms

The practical realization of DNA data storage is a major scientific goal. Here we introduce a simple, flexible, and robust data storage and retrieval method based on sequence alignment of the genomic DNA of living organisms. Duplicated data encoded by different oligonucleotide sequences was inserted redundantly into multiple loci of the Bacillus subtilis genome. Multiple alignment of the bit data sequences decoded by B. subtilis genome sequences enabled the retrieval of stable and compact data without the need for template DNA, parity checks, or error-correcting algorithms. Combined with the computational simulation of data retrieval from mutated message DNA, a practical use of this alignment-based method is discussed.     

Use of a computer data file for storage of heat resistance data on bacterial spores

The use of a computer data file to compile published heat resistance data on bacterial spores is described. Information relating to sporulation, heating and recovery of the spores, in addition to decimal reduction times at different temperatures has been stored. The data file was constructed using Minitab and an indexer program on a VAX 11/750 computer operating on VMS. Storage of the data in this way enables rapid manipulation and analysis of large quantities of information relating to heat resistance of bacterial spores.     

mz5: space- and time-efficient storage of mass spectrometry data sets

Across a host of MS-driven-omics fields, researchers witness the acquisition of ever increasing amounts of high throughput MS data and face the need for their compact yet efficiently accessible storage. Addressing the need for an open data exchange format, the Proteomics Standards Initiative and the Seattle Proteome Center at the Institute for Systems Biology independently developed the mzData and mzXML formats, respectively. In a subsequent joint effort, they defined an ontology and associated controlled vocabulary that specifies the contents of MS data files, implemented as the newer mzML format. All three formats are based on XML and are thus not particularly efficient in either storage space requirements or read/write speed. This contribution introduces mz5, a complete reimplementation of the mzML ontology that is based on the efficient, industrial strength storage backend HDF5. Compared with the current mzML standard, this strategy yields an average file size reduction to ～54% and increases linear read and write speeds ～3-4-fold. The format is implemented as part of the ProteoWizard project and is available under a permissive Apache license. Additional information and download links are available from http://software.steenlab.org/mz5.     

Optical CDMA system using bacteriorhodopsin for optical data storage

An optical CDMA (code division multiple access) system for the optical data storage using bacteriorhodopsin (BR) is reported as an application of the BR materials. The desired signal of multiple input can be recorded and reconstructed by use of orthogonal codes. An experimental setup is proposed and demonstrated.     

EXP-PAC: providing comparative analysis and storage of next generation gene expression data

Microarrays and more recently RNA sequencing has led to an increase in available gene expression data. How to manage and store this data is becoming a key issue. In response we have developed EXP-PAC, a web based software package for storage, management and analysis of gene expression and sequence data. Unique to this package is SQL based querying of gene expression data sets, distributed normalization of raw gene expression data and analysis of gene expression data across experiments and species. This package has been populated with lactation data in the international milk genomic consortium web portal (http://milkgenomics.org/). Source code is also available which can be hosted on a Windows, Linux or Mac APACHE server connected to a private or public network (http://mamsap.it.deakin.edu.au/~pcc/Release/EXP_PAC.html).     

One-step analysis of seed storage data and the longevity of Arabidopsis thaliana seeds

Seeds of two ecotypes of Arabidopsis thaliana, NW20 and N1601, were aged over a range of saturated salt solutions at temperatures between 6 degrees C and 55 degrees C. For each ecotype, the results from 37 storage experiments were summarized using the Ellis and Roberts viability equations and a modified version of these equations which allows for a proportion of 'non-respondents'. For both models, two approaches were taken in order to model the effect of moisture content (MC) and temperature on seed longevity. The first, a two-step approach, involved fitting individual survival curves and then multiple regression analysis of the fitted parameters on moisture content and temperature. For the second approach, the full viability models were fitted in one step, including the multiple regression for the effects of MC and temperature within the generalized linear model used to describe each survival curve. This one-step approach takes into account the full variability of the data and provides the best predictions of seed longevity based on the original assumptions of the Ellis and Roberts viability equations. As a consequence of taking into account all the variation, this one-step approach is more sensitive and thus more likely to detect changes due to reducing the number of parameters in the model as being significant. Whilst both approaches indicated that seeds from the two Arabidopsis ecotypes have the same response to MC and temperature, parameter values did differ between the approaches, with the one-step approach providing the better fit. The best model for these two ecotypes, from the one-step approach, confirmed a quadratic relationship between temperature and longevity, but the magnitude of the non-linearity is not as large as indicated by the universal value for the quadratic term.